Skyrim - Factions Expansion & Improvements

Thieve's Guild & Nightingales

• Opulent Thieves Guild + Opulent Thieves Guild - FPS Fix + Opulent Thieves Guild - Tweaks + Opulent Thieves Guild Patch Collection
• Thieves Guild Requirements SE  + Thieves Guild Reformation - Taking Care of Business + Thieves Guild Requirements SE - Droppable Stones (Optional Files)
• Thieves Guild Enhancements ("A thief's creed" only)
• Nightingale Hall Restored - Karliah as a Follower
• Revealing Rune
• Axarien's Animations - The Nightingales - Karliah Brynjolf
• Thieves Guild Dialogue Fix - USSEP Compatible
• Ryn's Goldenglow Estate
• More Thieves Caches
• Welcome Back to the Bee and Barb
• Following Mercer SSE
• The Ragged Flagon Merchants are Fences (Can buy stolen items)
• Thieves Guild Master Recognition
• Summerset Shadow Armor
• Weapon Animation (Nightingale Bow)
• Improved Shadowmarks (Textures only)
• JS Barenziah SE
• Iconic's Falmer Rosetta Stone
• Praedy's repository - SE - Grayfox Bust
• Business Ledger HD Retexture
• Kanjs - Falmer Statue - Particle light ENB - up to 4k
• Nocturnal's Portal HD
• Ebonmere Moons Restoration - ENB Light
• Iconic's Falmer Eye Gem Retexture (4K-2K)
• Resplendent Queen Bee Statue - 8K
• ElSopa HD - Skeleton Key SE
• Rally's Nightingale Clutter and Stones

Dark Brotherhood

• Listener's Initiates (Verified Creation)
• Innocence Lost - Quest Expansion
• Destroy The Dark Brotherhood - Quest Expansion
• Listen - Dark Brotherhood Radiant Quests
• Penitus Oculatus
• Fake Babette for Penitus Oculatus
• Realistic Dark Brotherhood Kidnapping (Location only)
• Dark Brotherhood Motivations
• Vittorias Alternate Wedding +  Vittorias Alternate Wedding - Patches
• Muiri's Revenge + Penitus Oculatus Patch
• Hidden DB Sanctuary Entrances
• Bald Astrid for Dark Brotherhood Ending
• Restoring the Aretino Residence SE
• Recruit Aventus to the Dark Brotherhood (There is a dialogue conflict with Innocence Lost Quest Expansion, Nothing major)
• Spaghetti's Faction Halls - Dark Brotherhood
• Statue of Sithis
• Dark Brotherhood Tenets 16K 8K 4K 2K 1K 512 Redone
• The Black Door - 3D Dagger and Glow - ENB Light
• Shadowmere Saddle Retexture
• Night Mother

Companions

• At Your Own Pace - Companions
• Improved Companions - Questline Tweaks (There is a compatibility issue with AYOP, It seems that you can't have Aela as your shield-sibling during Proving Honor. Nothing major)
• Companions Dialogue Bundle + Companions Conversation Bundle - At Your Own Pace Patch
• Follower Dialogue Expansion - Aela the Huntress
• Axarien's Animations - The Companions - Vilkas Farkas Aela
• Edmond's The Beast Within-Jorrvaskr Companion Werewolf Transformation
• Werewolf Spirits
• This Is Jorrvaskr - Home Of The Companions
• Skyforge Complete (JK's Skyrim And Whiterun Options)
• Rally's Werewolf Totems

There is The Conflict Under the Crescent - A Companions and Silver Hand Mod (Which makes you join the silver hand) but it is incompatible with most mods that change anything in the companions questline.

The College Of Winterhold

• Obscure's College of Winterhold + Obscure's College of Winterhold - Script Fix - cwhcm_setchangeonquestprog_03 + Obscure's College of Winterhold NPC Stuck in Staircase Fix +Obscure's College of Winterhold Arch-mage's Quarters Shadow Fix
• Obscure's College of Winterhold Addons
• Obscure's College of Winterhold Loot Rebalancing
• Immersive College NPCs
• Bibliophile's Arcanaeum - A Winterhold Circulating Collection
• Choose Your Own Arch-Mage
• Finding Velehk Sain
• Improved College Entry - Questline Tweaks (Always load this mod earlier than Misc. College of Winterhold Tweaks)
• Misc. College of Winterhold Tweaks
• College of Winterhold - Quest Expansion (This should be loaded after the two previous mods)
• The Midden - Expanded + Obscure's College of Winterhold - The Midden Extended Patch
• Respect for the Arch-Mage
• BUVARP SE RE - Chronicles of the College + Patches
• Catir's College Creatures 
• College of Winterhold Bridge Repaired
• Greater Saarthal for SSE + Greater Saarthal Tweaks and Fixes
• Weapon Animation (The Staff of Magnus)
• College of Winterhold - Glowing Symbols
• Statue of Shalidor - Mage Statue Replacer
• Skyking Shalidor 4k Textures
• Beautiful Sigils of Shalidor - 8k 4k 2k

Bards College 

• Bards College Expansion (Verified Creation)
• Spaghetti's Faction Halls - Bard's College.
• Bards College Expansion - Unofficial Patches

Civil War

• Open Civil War SSE + Serious Civil War Defense for OCW
• Serious Civil War Finale Sieges
• Civil War Aftermath SE
• Jarl Balgruuf Dilemma SSE + Serious Civil War Consequences for Jarl Balgruuf
• Neutral Civil War Forts Respawn
• After the Civil War - Siege Damage Repairs
• Civil War Deserters
• The Jagged Crown Tweaks
• Respect for the Legate
• Imperial Honor Guard + Imperial Honor Guard - Centurion Armor
• Imperial Rewards + Imperial Rewards - Compatibility and Integration Patches
• Whiterun without Main Quest - Civil War and Thane for Non-Dragonborn (Load after My Own Pace - Main Quest if you use it and disable AYOP-MQ's delay to Bleak Falls Barrow and Dragon Rising in that mod's MCM)
• Kynareth Replaces Talos - Civil War Consequence
• Spaghetti's Faction Halls - Castle Dour
• Rally's Civil War Document Tubes
• Rally's Battlemap Flags

Dawnguard

• Dawnguard - Tweaks and Enhancements (And the patches in the optional files)
• Sensible Dawnguard Prerequisite
• Dawnguard - Hall of Vigilant Requirement (And the optional patch)
• Castle Volkihar Rebuilt - SSE + what777's Castle Volkihar Rebuilt Patches
• Volkihar Travel - AddOn for Castle Volkihar Rebuilt
• Glorious Fort Dawnguard
• Immersive Dawnguard Dayspring Pass SE (IDDP)
• Serana's Tomb Blood Curse
• Dawnguard Don't Hunt Cured Vampires
• Serana Dialogue Edit - Skyrim Special Edition
• Weapon Animation (Auriel's Bow)
• JS Initiate's Ewer SE
• JS Bloodstone Chalice SE
• Iconic's Arvak Retexture
• Particle Lights for ENB - Moon Crests
• Vampire Lord Retexture - 8K
• Dawnguard Arsenal SSE (Heavy Armory also expands their weaponry, so I don't use it anymore)

East Empire Company

• East Empire Expansion (Verified Creation)
• High Visibility East Empire Logo
• East Empire Strongbox Logo SSE
• East Empire Company Armor
• East Empire Company Improved